Thanks for these insights, Lewis. In general, I agree with you that there is great uncertainty regarding externalized costs and that the number that emerges from any kind of methodical quantification exercise will be strongly influenced by subjective bias. The "intellectual barriers" you detail in the linked reference are valid and greatly reduce the degree of certainty which can be linked to any individual intellectual quantification of eternalized costs, but I would stop short of saying that such exercises are useless or even counter-productive.
Take climate change for example. It is true that the range of uncertainty surrounding the future impacts of climate change is huge, but the general consensus that these impacts are significant is important in itself. Progress has been slow, but there are now several CO2 pricing schemes in operation around the world and several others under development. The large body of scientific literature on the topic, albeit spread over a wide range, has certainly contributed greatly to the increasing degree to which the impacts of climate change on future generations are being accounted for.
As more real-world data becomes available and computational capacities and models improve, the uncertainty range will be gradually reduced. Clearly, it would be ill advised to completely abandon methodical analysis of the cost of CO2 because of the great uncertainties it entails. Doing so would slow down the societal response substantially, thus increasing the risk or irreversible negative impacts on the biocapacity of our planet.
In general, I see a strong necessity to include externalized costs in this project for the sake of completeness. Even though there is a very large uncertainty range, there is a general consensus that externalized costs are real. If some estimate of these costs is not included, any comparative assessment of different energy options would be unfairly biased towards low-cost fossil fuels like coal. If the range of estimates received varies widely, that is a conclusion in itself. One thing I am certain of though is that the median estimate of externalized costs will be significant (and positive) for the majority of energy options evaluated in this project.